Universität zu Köln

Choi, Young-Joon, Beakes, Gordon, Glockling, Sally, Kruse, Julia, Nam, Bora, Nigrelli, Lisa, Ploch, Sebastian ORCID: 0000-0002-7129-4523, Shin, Hyeon-Dong, Shivas, Roger G., Telle, Sabine, Voglmayr, Hermann ORCID: 0000-0001-7666-993X and Thines, Marco (2015). Towards a universal barcode of oomycetes - a comparison of the cox1 and cox2 loci. Mol. Ecol. Resour., 15 (6). S. 1275 - 1289. HOBOKEN: WILEY. ISSN 1755-0998

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Abstract

Oomycetes are a diverse group of eukaryotes in terrestrial, limnic and marine habitats worldwide and include several devastating plant pathogens, for example Phytophthora infestans (potato late blight). The cytochrome c oxidase subunit 2 gene (cox2) has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. The cox1 locus has been used in some studies of Pythium and Phytophthora, but has rarely been used for other oomycetes, as amplification success of cox1 varies with different lineages and sample ages. To determine which out of cox1 or cox2 is best suited as a universal oomycete barcode, we compared these two genes in terms of (i) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (ii) sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding-type material. Sequence data for several historic type specimens exist for cox2, but there are none for cox1. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. The cox2-1 spacer could be a useful marker below species level. Improved protocols and universal primers are presented for all genes to facilitate future barcoding efforts.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Choi, Young-Joon UNSPECIFIED UNSPECIFIED UNSPECIFIED Beakes, Gordon UNSPECIFIED UNSPECIFIED UNSPECIFIED Glockling, Sally UNSPECIFIED UNSPECIFIED UNSPECIFIED Kruse, Julia UNSPECIFIED UNSPECIFIED UNSPECIFIED Nam, Bora UNSPECIFIED UNSPECIFIED UNSPECIFIED Nigrelli, Lisa UNSPECIFIED UNSPECIFIED UNSPECIFIED Ploch, Sebastian UNSPECIFIED orcid.org/0000-0002-7129-4523 UNSPECIFIED Shin, Hyeon-Dong UNSPECIFIED UNSPECIFIED UNSPECIFIED Shivas, Roger G. UNSPECIFIED UNSPECIFIED UNSPECIFIED Telle, Sabine UNSPECIFIED UNSPECIFIED UNSPECIFIED Voglmayr, Hermann UNSPECIFIED orcid.org/0000-0001-7666-993X UNSPECIFIED Thines, Marco UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-388907
DOI:	10.1111/1755-0998.12398
Journal or Publication Title:	Mol. Ecol. Resour.
Volume:	15
Number:	6
Page Range:	S. 1275 - 1289
Date:	2015
Publisher:	WILEY
Place of Publication:	HOBOKEN
ISSN:	1755-0998
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language CYTOCHROME-OXIDASE-II; ALBUGO-CANDIDA COMPLEX; SUDDEN OAK DEATH; PHYLOGENETIC-RELATIONSHIPS; MOLECULAR PHYLOGENY; DOWNY MILDEWS; PHYTOPHTHORA-RAMORUM; EXCEPTIONAL LENGTH; SEQUENCE-ANALYSIS; PERONOSPORA Multiple languages Biochemistry & Molecular Biology; Ecology; Evolutionary Biology Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/38890